Alphaviruses contains a linear, positive sense, single stranded RNA genome of approximately 11.8 kb. Their RNA genome consists of a capped 5′ non-coding region (NCR) and 3′ polyadenylated NCR. The non-structural proteins i.e. nsP1, nsP2, nsP3 & nsP4 are required for virus replication whereas structural proteins i.e. E1, E2, E3 and 6K forms part of capsid and envelope. Given the similarity of Chikungunya virus genomic structure with those of other alphaviruses, Chikungunya virus is expected to encode spikes on the virion surface that is each formed by the three E1-E2 heterodimers; where E1 glycoprotein mediates fusion and the E2 glycoprotein interact with the host receptor. These structural and non-structural proteins are critical for the entry and multiplication of alpha-virus in the host cell and therefore represent rational targets for antiviral therapy.
RNA interference (RNAi) is the process of sequence specific Post Transcriptional Gene Silencing (PTGS) in Eukaryotes. In RNAi, long dsRNA and miRNA precursors are processed to small interfering RNA (siRNA)/microRNA duplexes by the RNaseIII-like enzyme Dicer. The siRNA/miRNA duplexes thus formed then binds with other components in cell to form a nucleic acid-protein complex called RNA-induced silencing complex (RISC). The activated RISC targets a homologous mRNA by base pairing, resulting in the cleavage and degradation of the mRNA inhibiting cell-specific gene expression. In eukaryotes, RNAi not only regulates the gene expression but also acts as a cellular defence mechanism against invaders including viruses like Poliovirus, HIV, Hepatitis, Chikungunya etc. In recent years inhibition of specific genes by RNAi has proven to be a potential therapeutic strategy against viral infections. For instance, inhibition of virus replication and gene expression by directly introducing RNAi agents into the cells have been reported for several RNA viruses including several important human pathogens such as HIV, Hepatitis, Influenza virus etc. It has also been shown that alphaviruses such as Selmiki Forest Virus, Venezuelan equine encephalitis are susceptible to RNAi action.
Chikungunya virus is a mosquito transmitted alpha-virus belonging to family Togaviridae. Chikungunya virus is responsible for an acute infection characterized by high fever, arthralgia, myalgia, headache, rash etc. Although of immense medical importance, no effective, vaccine or specific therapy is available.
Dash et al in ‘RNA interference mediated inhibition of Chikungunya virus replication in mammalian cells’; Biochemical and Biophysical Research Communications; September 2008] have demonstrated that introduction of exogenous siRNA can inhibit replication of Chikungunya virus in-vitro. However, success of this study is limited as siRNAs used against ns3 and E1 genes of Chikungunya virus were shown to reduce replication by 65% by 48 h post infection and not evaluated in-vivo. Also, Lam et al in ‘Expression of Plasmid-Based shRNA against the E1 and nsP1 Genes Effectively Silenced Chikungunya virus replication’; PLOS ONE; October 2012 have demonstrated the effective antiviral strategy against Chikungunya virus infection in-vitro & in-vivo, targeting E1 and nsP1 genes using shRNA.
These results indicate the potential use of novel strategies using RNAi against the structural and non structural proteins of alphaviruses. E2 and nsP1 genes are highly conserved in Chikungunya virus strains and are important in entry and multiplication in host cell and, therefore, represent rational targets for antiviral therapy i.e. inhibition of Chikungunya virus.